Contacts of the strand formed by residues 571 - 578 (chain A) in PDB entry 5NC5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 571 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A TYR* 3.9 29.2 - - + +
328A ASP 4.1 26.2 - - - +
329A THR* 4.9 8.3 - - + -
569A GLN* 4.1 20.8 - - + +
570A GLY* 1.3 86.8 + - - +
572A PHE* 1.3 69.7 + - - +
629A VAL 3.3 12.1 - - - +
630A SER* 3.6 18.2 - - - +
631A LEU* 4.5 1.2 - - - +
644A VAL* 4.4 3.9 - - - +
667A ASN* 4.2 11.8 - - - +
668A LEU 5.8 0.2 + - - -
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Residues in contact with PHE 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 4.1 5.4 - - - -
571A VAL* 1.3 78.4 - - - +
573A MET* 1.3 76.0 + - - +
574A THR* 3.9 3.6 - - - -
598A TYR* 3.6 41.5 - + - -
606A VAL* 5.1 0.2 - - + -
628A PHE* 3.9 0.2 - - - -
629A VAL* 2.9 56.6 + - + +
631A LEU* 3.5 28.3 - - + -
644A VAL* 4.2 16.2 - - + -
647A ILE* 3.8 20.2 - - + -
648A THR* 3.9 14.6 - - - -
665A ALA* 4.1 9.6 - - + -
666A PHE 3.8 13.0 - - - +
667A ASN* 4.7 2.0 - - - +
668A LEU 5.9 1.3 - - - +
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Residues in contact with MET 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A SER* 6.0 0.9 - - - -
136A PHE* 5.0 4.3 - - - +
327A TYR* 4.0 19.7 - - + +
572A PHE* 1.3 81.7 - - - +
574A THR* 1.3 67.7 + - - +
617A PHE* 4.0 21.3 - - + -
626A ILE* 3.9 16.2 - - + -
627A ALA 3.4 5.2 - - - +
628A PHE* 3.5 37.9 - - + -
665A ALA* 3.7 0.5 - - - -
666A PHE* 3.2 51.7 + - + +
668A LEU* 3.4 35.4 - - + -
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Residues in contact with THR 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A PHE* 3.9 3.3 - - - -
573A MET* 1.3 81.0 + - - +
575A MET* 1.3 66.0 + - - +
576A VAL* 4.6 2.3 - - + +
594A VAL* 4.4 9.0 - - + -
598A TYR* 2.6 32.1 + - - +
626A ILE* 3.4 6.9 - - - +
627A ALA* 2.8 45.1 + - - +
629A VAL* 4.4 1.0 - - - +
655A PHE* 4.0 16.2 - - + -
663A VAL* 4.5 3.6 - - + -
664A PHE 3.4 21.8 - - - +
665A ALA* 3.9 3.8 - - - +
666A PHE* 4.5 0.7 - - - -
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Residues in contact with MET 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A THR* 1.3 74.8 - - - +
576A VAL* 1.3 64.2 + - - +
577A GLN* 3.2 41.5 - - + +
616A GLY* 5.5 4.7 - - - -
617A PHE* 5.1 21.3 - - + +
618A ALA* 6.0 1.1 - - + -
624A THR* 4.7 4.7 - - - +
625A GLY 4.0 8.7 - - - +
626A ILE* 4.6 6.1 - - + +
662A MET* 3.9 1.2 - - - +
663A VAL* 3.4 5.2 - - - +
664A PHE* 3.1 67.1 + - + -
666A PHE* 3.9 11.3 - - + -
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Residues in contact with VAL 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A THR* 4.6 5.6 - - + +
575A MET* 1.3 79.6 - - - +
577A GLN* 1.3 62.9 + - - +
578A LEU* 4.0 16.6 - - + -
587A THR* 4.9 7.9 - - + +
590A VAL* 3.9 26.2 - - + -
591A LEU* 4.2 18.2 - - + -
594A VAL* 3.9 27.4 - - + -
624A THR* 3.4 6.6 + - - -
625A GLY* 3.0 40.7 + - - +
626A ILE 5.4 0.2 - - - -
627A ALA 5.5 0.2 - - - +
662A MET 3.7 2.2 - - - -
663A VAL* 4.4 8.7 - - + +
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Residues in contact with GLN 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575A MET* 3.2 34.9 - - + +
576A VAL* 1.3 75.4 - - - +
578A LEU* 1.3 68.5 + - - +
579A PRO* 4.8 0.2 - - - +
618A ALA* 4.4 14.1 - - - +
623A ASN* 3.1 27.3 + - - +
624A THR* 3.4 24.8 + - - +
661A ALA* 3.4 4.0 - - - +
662A MET* 2.6 55.0 + - + +
721A LEU* 3.4 24.4 - - - +
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Residues in contact with LEU 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A VAL* 4.0 20.2 - - + -
577A GLN* 1.3 79.3 + - - +
579A PRO* 1.3 72.3 - - + +
580A ALA 3.3 0.5 + - - -
582A ALA* 3.3 26.5 - - + -
586A ARG* 3.9 18.8 - - + +
587A THR* 3.6 32.5 - - - +
590A VAL* 3.8 24.0 - - + -
623A ASN* 3.0 32.9 + - - +
660A ASP 3.9 11.9 - - - +
661A ALA* 4.0 7.4 - - + -
721A LEU* 5.1 0.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il